Abstract: Embodiments disclose methods, systems, and computer-readable media for accelerated base calling of sequencing data. These methods may be adapted to accelerate sequence determination for data arising from a variety of different nucleic acid sequencing platforms. In various embodiments, configurable logic circuits such as FPGAs and GPUs may be adapted to perform raw signal processing, basecalling, and/or sequence determination operations providing further enhancements to the sequence analysis methods.

Abstract: The invention provides particle compositions having applications in nucleic acid analysis. Nucleic acid polymer particles of the invention allow polynucleotides to be attached throughout their volumes for higher loading capacities than those achievable solely with surface attachment. In one aspect, nucleic acid polymer particles of the invention comprise polyacrylamide particles with uniform size distributions having low coefficients of variations, which result in reduced particle-to-particle variation in analytical assays. Such particle compositions are used in various amplification reactions to make amplicon libraries from nucleic acid fragment libraries.

Abstract: A filter assembly for separating microcarriers from a fluid medium includes a collapsible container bounding a sterile compartment adapted to hold a fluid. An inlet port is attached to the container through which fluid flows into the compartment. An outlet port is attached to the container through which fluid flows out of the compartment. A filter is disposed within the compartment, the filter dividing the compartment into an inlet chamber that is fluidly coupled with the inlet port and an outlet chamber that is fluidly coupled with the outlet port, the filter allowing a medium to pass therethrough but preventing microcarriers disposed in the medium from passing therethrough.

Abstract: The present disclosure provides methods, compositions, kits, and systems useful in the determination and evaluation of the immune repertoire using genomic DNA from a biological sample. In one aspect, target-specific primer panels provide for the effective amplification of sequences of T cell receptor and/or B cell receptor chains with improved sequencing accuracy and resolution over the repertoire. Nucleic acid sequences of variable regions associated with the immune cell receptor are determined to effectively portray clonal diversity of a biological sample and/or differences associated with the immune cell repertoire of a biological sample.

Abstract: A method of mixing a fluid includes at least partially unfolding a collapsible bag bounding a compartment, the collapsible bag containing in the compartment at least a portion of an elongated drive line or drive shaft and an impeller secured to the drive line or drive shaft, the impeller including a plurality of impeller blades that are pivotable relative to the drive line or drive shaft, at least one of the plurality of impeller blades being in a collapsed position. A fluid is delivered into the compartment of the collapsible bag. The drive line or drive shaft is then rotated so as to rotate the impeller within the compartment and mix the fluid therein, the at least one of the plurality of impeller blades pivoting from the collapsed position to an expanded position as the impeller is rotated within the compartment.

Abstract: The present set of embodiments relate to a bioproduction system, method, and apparatus for creating a scalable bioreactor system. Specifically, the present set of embodiments enable the determination of bioreaction performance characteristics of a commercial scale by matching operational parameters between a small test scale bioreaction to that of a commercial scale bioreaction. The system and methods do not rely on simply making bioreactor apparatuses across scales the same dimensionally which would not account for differences in fluid dynamic properties between very small to very large volumes, but requires tuning of a variety of systems (mixing assembly, sparger system, and headspace airflow system) in conjunction with one another to achieve predictive outcomes.

Abstract: The present disclosure provides methods, compositions and kits as well as systems for manipulating nucleic acids, including implementing isothermal amplification, such as recombinase-polymerase amplification (RPA), of a nucleic acid template using a pre-seeded solid support. Provided are rapid and efficient methods for generating template nucleic acid molecules comprising specific nucleotide sequence bound to solid support. Such methods can be used, for example, in manipulating nucleic acids in preparation for analysis methods that utilize monoclonal populations of nucleic acids.

Abstract: A magnetic particle separation system includes a magnetic field generating device having an upper surface with a receiving area formed thereon; and a magnetic field generating element disposed beneath the upper surface, the magnetic field generating element being configured to produce a magnetic field above the upper surface. A container assembly is disposed on the upper surface and includes: a flexible container having an outer wall with an interior surface that at least partially bounds an internal compartment, the outer wall having a front side and an opposing back side with the internal compartment disposed therebetween; a fluid inlet extending through the outer wall at the front side; a fluid outlet extending through the outer wall at the front side; and a first partition projecting into the internal compartment from the front side between the fluid inlet and the fluid outlet.

Abstract: The present disclosure provides compositions, methods, kits, systems and apparatus that are useful for nucleic acid polymerization. In particular, modified polymerases and biologically active fragments thereof, such as modified Taq polymerases, are provided that allow for improved nucleic acid amplification. In some aspects, the disclosure provides modified polymerases having improved thermostability, accuracy, processivity and/or read length as compared to a referenceTaq polymerase. In some aspects, the disclosure relates to modified polymerases or biologically active fragments thereof, useful for amplification methods, and in practically illustrative embodiments, emulsion PCR.

Abstract: A liquid mixing system includes a support housing at least partially bounding a compartment. A mount is secured to the support housing. A drive motor assembly is configured to engage a drive shaft for moving the drive shaft within the compartment of the support housing. A four bar linkage system extends between the mount and the drive motor assembly, the four bar linkage system being movable between a first position wherein the drive motor assembly is disposed at a first elevation and a second position wherein the drive motor assembly is disposed at a second elevation that is different from the first elevation.

Abstract: The disclosure generally relates to compositions and methods for the production of nucleic acid molecules. In some aspects, the invention allows for the microscale generation of nucleic acid molecules, optionally followed by assembly of these nucleic acid molecules into larger molecules. In some aspects, the invention allows for efficient production of nucleic acid molecules (e.g., large nucleic acid molecules such as genomes).

Abstract: An optical detection system for a capillary electrophoresis instrument is disclosed. The optical detection system comprises an ultraviolet (UV) source and an absorption measurement optical path. The optical path comprises a first plurality of optical elements comprising a first optical fiber array and other elements. The first plurality of optical elements are arranged to obtain a plurality of respective UV beamlets from a UV beam emitted by the UV source and to direct, at least partially using the first optical fiber array, the respective UV beamlets through respective capillaries of a plurality of capillaries and to an absorption detector positioned to detect respective signals for use in obtaining respective UV absorption measurements corresponding to the respective capillaries.

Abstract: Compositions and methods are described for preparing media, feeds, and supplements. Such methods and medias may display increased stability of labile components and may use, for example, microsuspension and/or encapsulation technologies, chelation, and optionally, coating and/or mixing the labile compounds with anti-oxidants. The compositions may withstand thermal and/or irradiation treatment and have reduced virus number. These techniques may result in product with extended shelf-life, extended release of their internal components into culture, or in product that can be added aseptically into a bioreactor using minimal volumes. The compositions and methods may optimize the bioproduction workflow and increase efficiency.

Abstract: A high data rate integrated circuit, such as an integrated circuit including a large sensor array, may be implemented using clock multipliers in individual power domains, coupled to sets of transmitters, including a transmitter pair configuration. Reference clock distribution circuitry on the integrated circuit distributes a relatively low speed reference clock. In a transmitter pair configuration, each pair comprises a first transmitter and a second transmitter in a transmitter power domain. Also, each pair of transmitters includes a clock multiplier connected to the reference clock distribution circuitry, and disposed between the first and second transmitters, which produces a local transmit clock.